How should one list on a resume time and experience gained while working for a covert alphabet agency?

To protect the identity and security of one's self (and others), an individual's true identity was known only to his/her handler, so in working deep cover in particular assignments, there exists no paper trail, and although possessing a security clearance higher than TS, i.e. NTK, the agent was/is a phantom respecting verification of identity and experience. After leaving the aforementioned agency, the client is concerned about: (A) Accounting for the time worked in this agency, (B) Documentary proof of pertinent, and varied, training and skills learned while in the employment of THE AGENCY, or during assignments when placed within cover jobs, as part of classified operations designated to assess, and/or gain information respecting organizations, businesses, and/or individuals working for, or involved in, projects with agencies of the U.S. government, and (C) Because the client signed a Confidentiality Agreement, what impact does this have as respects prospects for future employment?

This is a little confusing...
But I guess I would say that I bought and watched all the old school Sesame Street episodes and insist I was up on my knowledge of the alphabet.
Good luck!

In agreeing to work for said covert agency that individual would have signed an agreement of non-disclosure relinquishing their right to claim employment by the, ahem, non-existent agency and the time employed there.

That's the price for being a spy.